DESCRIPTION

This is a wrapper for running the QuickTree application by Kevin Howe. You can download it here: http://www.sanger.ac.uk/Software/analysis/quicktree/

Currently only input with alignments and output of trees is supported. (Ie. no support for distance matrix in/out.)

You will need to enable this QuickTree wrapper to find the quicktree program. This can be done in (at least) three ways:

1. Make sure the QuickTree executable is in your path.
2. Define an environmental variable QUICKTREEDIR which is a
directory which contains the 'quicktree' application:
In bash:
export QUICKTREEDIR=/home/username/quicktree_1.1/bin
In csh/tcsh:
setenv QUICKTREEDIR /home/username/quicktree_1.1/bin
3. Include a definition of an environmental variable QUICKTREEDIR in
every script that will use this QuickTree wrapper module, e.g.:
BEGIN { $ENV{QUICKTREEDIR} = '/home/username/quicktree_1.1/bin' }
use Bio::Tools::Run::Phylo::QuickTree;

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _